Well, there is no difference between trilin or nearest. mri_vol2surf displays segfault regardless which option I use (trilin or nearest).
On Thu, 10 Apr 2014 11:30:38 -0400 Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
I don't understand what the question is. If you need to interpolate, then use --interp trilinear doug
On 04/10/2014 04:36 AM, Joerg Pfannmoeller wrote:
Allright! The only point I would like to emphasize is:
Regardless if option trilin or nearest is used I need to interpolate the functional data to the structural image of the subject. This might be due to a feature of the function "build_sample_array" in the "mri_vol2surf" source code. In this function there are some constant values (din = 1.0, dout = 0.1, nsamples = 10), which might be the reason why I need to interpolate the functional data to the structural image. Currently I can not investigate the code any further. Do you have enough experience with the source code to clarify this question?
On Wed, 09 Apr 2014 09:31:57 -0400 Douglas Greve greve@nmr.mgh.harvard.edu wrote:
You can use --projfrac (which can perform an interpolation with --interp trilinear)
On 4/9/14 2:44 AM, Joerg Pfannmoeller wrote:
Sorry for this question, but now I am confused. Do you mean that I should not use projopt and just use the interpolation? If so why should I not use projfrac?
On Tue, 08 Apr 2014 15:02:36 -0400 Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You'll have to do without it for now and just do the interpolation
On 04/08/2014 03:32 AM, Joerg Pfannmoeller wrote:
Well, I need to use that option. In this case I will just interpolate to the 1 mm grid and proceed this way.
On Mon, 07 Apr 2014 12:14:47 -0400 Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
> Sorry, I don't understand. You mean it still segfaults without --projopt > or that you have to use projopt? > > On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote: >> Unfortunately that is no option for me. >> >> >> >> On Fri, 04 Apr 2014 15:33:47 -0400 >> Douglas N Greve greve@nmr.mgh.harvard.edu wrote: >> >>> Don't use --projopt and it won't segfault >>> >>> On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote: >>>> The command is: >>>> >>>> mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex >>>> >>>> The output is the follwoing: >>>> >>>> >>>> srcvol = /.../f001.nii >>>> srcreg = /.../register.f001.dof6.dat >>>> srcregold = 0 >>>> srcwarp unspecified >>>> surf = white >>>> hemi = rh >>>> trgsubject = subjid >>>> surfreg = sphere.reg >>>> reshape = 0 >>>> interp = nearest >>>> float2int = round >>>> GetProjMax = 0 >>>> INFO: float2int code = 0 >>>> INFO: changing type to float >>>> Done loading volume >>>> Loading label /.../label/rh.cortex.label >>>> Reading surface /.../surf/rh.white >>>> Done reading source surface >>>> Reading thickness /.../surf/rh.thickness >>>> Done >>>> Mapping Source Volume onto Source Subject Surface >>>> reading gm volume fraction from /.../map001.gm.mgz >>>> reading wm volume fraction from /.../map001.wm.mgz >>>> reading csf volume fraction from /.../map001.csf.mgz >>>> mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault >>>> >>>> Do you have an idea about the cause of the error? >>>> >>>> >>>> >>>> >>>> >>>> On Wed, 02 Apr 2014 17:28:14 -0400 >>>> Douglas N Greve greve@nmr.mgh.harvard.edu wrote: >>>> >>>>> what is your command line that is seg faulting? What is the terminal output? >>>>> >>>>> On 04/02/2014 05:17 PM, pfannmoelj@uni-greifswald.de wrote: >>>>>> Please help me with this issue: >>>>>> >>>>>> If I apply mri_surf2vol to a single volume of unprocessed epi-data, it >>>>>> results in a segmentation fault. It works if I apply mri_vol2vol for >>>>>> registration of epi and anatomy, but than an interpolation is >>>>>> involved. I would like to avoid the interpolation and apply >>>>>> mri_surf2vol directly to the unprocessed data in order to minimize the >>>>>> number of interpolations. >>>>>> >>>>>> >>>>>> At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote: >>>>>> >>>>>> This is something BF added Sept 1 2009: >>>>>> >>>>>> added --projopt switch to do optimal linear estimation of gray matter >>>>>> values given a set of precomputed gray matter densities. >>>>>> >>>>>> I don't know what it would mean beyond that >>>>>> >>>>>> doug >>>>>> >>>>>> >>>>>> On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote: >>>>>> > Hello, >>>>>> > >>>>>> > I found an option in mri_vol2surf for which I could not find a >>>>>> documentation. The option is called: >>>>>> > >>>>>> > --projopt >>>>>> > >>>>>> > It would be nice if somebody could give a description of this >>>>>> option. >>>>>> > >>>>>> > Respectfully yours >>>>>> > >>>>>> > pfannmoe >>>>>> > >>>>>> > >>>>>> > _______________________________________________ >>>>>> > Freesurfer mailing list >>>>>> > Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> > >>>>>> > >>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> Outgoing: >>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to >>>>>> whom it is >>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>> the e-mail >>>>>> contains patient information, please contact the Partners >>>>>> Compliance HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>> you in error >>>>>> but does not contain patient information, please contact the >>>>>> sender and properly >>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve@nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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